- compbio-allhands@cgl.ucsf.edu - RBVI Mailing Lists

[Compbio-allhands] Fwd: Computational Biology Position
by Brian Shoichet 08 Apr '16

08 Apr '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Susie Stephens" <susie.stephens(a)gmail.com> Date: Apr 9, 2016 1:33 AM Subject: Computational Biology Position To: <bshoichet(a)gmail.com> Cc: Hi Brian, How are you doing? Are you aware of any computational biologists with 2-5 years of experience who would be interested in working at Pfizer with a focus on target discovery and validation in oncology and immuno-oncology? If you know of someone it would be great if you could point them in my direction, or have them apply for the job at https://globaljobs.pfizer.com/pages/jobs.aspx using Job Id 1010987. Thanks for you rhelp. Best, Susie

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[Compbio-allhands] 4/14/16 Seminar with Ian Wilson- NOTE LOCATION
by Flowers, Nicole 08 Apr '16

08 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall N114 NO SIMULCAST. URL for live capture will be sent out on 4/13/16. HARC Center Speaker: Ian Wilson Scripps Broad neutralization of viral pathogens April 14, 2016 B. Stroud, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: job opportunity in Seattle area
by Jacobson, Matthew 05 Apr '16

05 Apr '16

- Matt Begin forwarded message: From: Jaline Gerardin <gerardin(a)gmail.com<mailto:gerardin@gmail.com>> Subject: job opportunity in Seattle area Date: April 5, 2016 at 9:17:13 PM PDT To: Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, We have an interesting position open at the interface of software and research. Could you forward to compbio-allhands? thanks, Jaline -------------------------------------------------------------------------------------------------- Open position at Institute for Disease Modeling, Bellevue WA: The IDM Research Software Engineer will work on an elite team of software developers along with testers and researchers at IDM tasked with developing software tools for all stages of the disease modeling pipeline. This pipeline includes designing and querying large data for climate, demographic, and transportation data for input to the disease modeling software; specifying and commissioning simulation jobs on a high performance computing cluster; detailed simulation of disease transmission dynamics; data reduction and analysis of simulation output; and workstation and web based data visualization tools. This position focuses on building tools and applications to support the different disease teams. Full job posting: http://iv.avature.net/careers/JobDetail/Bellevue-Wa-Washington-United-State… Institute for Disease Modeling: www.idmod.org<http://www.idmod.org/>

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[Compbio-allhands] Fwd: Hands-On Computer Aided Drug Design Workshop @ UCSF, San Francisco - Friday Apr. 15
by Jacobson, Matthew 05 Apr '16

05 Apr '16

I don’t recall whether this has been distributed on this list previously If you want to learn MOE ... - Matt Begin forwarded message: From: Audrey Bonin <abonin(a)chemcomp.com<mailto:abonin@chemcomp.com>> Subject: Hands-On Computer Aided Drug Design Workshop @ UCSF, San Francisco - Friday Apr. 15 Date: April 5, 2016 at 11:33:07 AM PDT To: Audrey Bonin <abonin(a)chemcomp.com<mailto:abonin@chemcomp.com>> Dear Friends and Colleagues , I would like to invite you to our hands-on computer-aided drug design workshops which will take place at UCSF - April 15th, 2016. The workshops are open to the public and all interested parties are welcome to attend - no prior software experience is required to participate. Please find course information and related details below. The workshop is free but pre-registration is required since places are limited, to register please visit : http://www.chemcomp.com/Workshops-North_America.htm Lunch, and refreshments will be provided during the workshops, please bring your own laptop to the workshop*. Date: CCG Workshops - Friday April 15, 2016 Location: UCSF - Smith Cardiovascular Research Bldg (CVRI), 555 Mission Bay Blvd S., first floor seminar room. ================================================================ 08:30-09:00 Morning break* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 09:00-12:00 Structure-Based Drug Design and Ligand Modification Molecular Surfaces and Maps / Ligand Interactions / Conformational Searching / Ligand Optimization / Ligand Selectivity / Protein Alignments and Superposition - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 12:00-13:00 Lunch* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -- - - - 13:00-17:00 Antibody Modeling and Protein Engineering in MOE Protein-Protein Interactions / Protein Properties / Developability / Hot Spot Analysis / Antibody Modeling / Molecular Surfaces / Protein-protein docking ================================================================ *Continental breakfast and lunch will be provided. ================================================================ -- Course title: Structure-Based Drug Design and Ligand Modification Course description: The course covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Conformational searching and analysis of the ligand to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied. Course title: Antibody Modeling and Protein Engineering in MOE Course description: The course covers approaches for structure-based biologics design and includes protein-protein interactions analysis, in silico protein engineering, affinity modeling and antibody homology modeling. The interaction of a co-crystallized antibody-antigen complex will be evaluated by generating and examining the molecular surface topology and visualizing protein-protein interactions in 3D and 2D. The application of protein engineering tools for homology modeling and conducting property optimization of an antibody-antigen complex in the context developability will be studied.All the steps necessary for producing and assessing antibody homology models will be described. Methods for evaluating the structure of protein and antibody models will be discussed. *If you don't have access to MOE, please communicate with me prior to the workshop, I will set up a demo key for you so you can follow along on your personal laptop. Regards, Audrey Bonin, M. Sc. Chemistry Academic Services Manager Chemical Computing Group T. +1 514 393-1055<tel:%2B1%20514%20393-1055> abonin(a)chemcomp.com<mailto:abonin@chemcomp.com> | www.chemcomp.com<http://www.chemcomp.com/> Follow us on Twitter! @CCG_MOE

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[Compbio-allhands] Fwd: Editorial
by Brian Shoichet 03 Apr '16

03 Apr '16

---------- Forwarded message ---------- From: Patrick Walters <wpwalters(a)gmail.com> Date: Sun, Apr 3, 2016 at 8:29 AM Subject: Re: Editorial To: Brian Shoichet <shoichet(a)cgl.ucsf.edu> W e're looking for someone with MD expertise (see below). I think this could be a huge opportunity for someone of that phenotype. Please let me know if you know of anyone who would be interested in joining our band. Best, Pat ------- Relay Therapeutics is seeking a highly motivated computational chemist to join our rapidly growing team. This individual will utilize cutting edge computational methods, in conjunction with information generated by a variety of biophysical techniques, to design novel therapeutics targeted to allosteric sites. In this role, the ideal candidate will work as part of a multidisciplinary team to integrate computational and experimental insights and drive drug discovery. *Responsibilities* - Carry out analyses that combine computational and experimental data to develop testable hypotheses that drive drug discovery programs - Collaborate with scientists throughout the company to maximize the impact of computational efforts on projects - Work collaboratively with external computational groups to develop and refine new computational methods - Ensure effective communication of computational results across departments and teams - Develop new approaches to streamline and enhance computational workflows *Preferred Qualifications* - Ph.D. in Computational Chemistry, Computational Biology, Biophysics, or a related discipline - 1 to 5 years of industrial or postdoctoral experience - Demonstrated expertise applying wide variety of modern computational chemistry methods - Demonstrated expertise in structure-based drug design - In depth knowledge of molecular dynamics and its application to drug discovery - Facility working in a Unix/Linux environment - Ability to program in at least 1 modern scripting language (e.g. Python) - Strong interpersonal and communications skills - Ability to conduct independent research >>>> >>>> -- Brian Shoichet, Professor http://bkslab.org/ <http://www.uoft.bkslab.org/> 415-514-4126 University of California, San Francisco Dept. of Pharmaceutical Chemistry By Courtesy: University of Toronto, Faculty of Pharmacy Ontario Institute for Cancer Research

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[Compbio-allhands] 4/7/16 Seminar with Ronen Marmorstein
by Flowers, Nicole 01 Apr '16

01 Apr '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Ronen Marmorstein University of Pennsylvania Molecular mechanisms of post-translational and co-translational protein acetylation April 7, 2016 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoc openings
by Matt Jacobson 29 Mar '16

29 Mar '16

Positions at Livermore national lab -- Matt Sent from my iPhone Begin forwarded message: From: "Wong, Sergio E." <wong105(a)llnl.gov<mailto:wong105@llnl.gov>> Date: March 29, 2016 at 4:33:31 PM EDT To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Subject: Postdoc openings Hi; Here are the links to two postdoc positions in our group: http://careers-ext.llnl.gov/jobs/5183154-postdoctoral-research-staff-member… http://careers-ext.llnl.gov/jobs/5183258 Thanks; -Sergio

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[Compbio-allhands] Fwd: Summer internship opportunity in CompBio at Bayer for distribution
by Andrej Sali 24 Mar '16

24 Mar '16

> Begin forwarded message: > > From: Shaun Lippow <shaun.lippow(a)bayer.com> > Subject: Summer internship opportunity in CompBio at Bayer for distribution > Date: March 24, 2016 at 10:32:37 AM PDT > To: "sali(a)salilab.org" <sali(a)salilab.org> > > Dear Andrej, > > I’m a senior scientist at Bayer in Mission Bay and am requesting help to distribute a summer internship opportunity in computational biology for an upper-level undergrad or a graduate student. The topic is our sequence-based immunogenicity prediction, which I know is of interest to your lab or at least complementary to the structure-based MHC/TCR approach. > > I’ve attached the internship description. Applicants should apply through our company website (not directly to me): > https://career.bayer.us/job/Computational-Biology-Summer-Intern--0000159445… <https://career.bayer.us/job/Computational-Biology-Summer-Intern--0000159445…> > > Best regards, > Shaun > > > > > The information contained in this e-mail is for the exclusive use of the intended recipient(s) and may be confidential, proprietary, and/or legally privileged. Inadvertent disclosure of this message does not constitute a waiver of any privilege. If you receive this message in error, please do not directly or indirectly use, print, copy, forward, or disclose any part of this message. Please also delete this e-mail and all copies and notify the sender. Thank you. > > For alternate languages please go to http://bayerdisclaimer.bayerweb.com <http://bayerdisclaimer.bayerweb.com/> > >

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[Compbio-allhands] postdoc fellow position
by Hao Li 16 Mar '16

16 Mar '16

*FYI. * * * *Postdoctoral Fellow position in Computational Biology and Bioinformatics* We are seeking for a highly motivated postdoctoral fellow, who has good programming skills and extensive genomics/epigeneomics data analysis experience, to study transcriptional regulation networks in mammalian systems using ChIP-seq, RNA-seq and Hi-C data. Candidates should send CV and arrange to have 3 letters of recommendation letters sent directly to michael.zhang(a)utdallas.edu <mailto:michael.zhang@utdallas.edu>. Michael Zhang, Ph.D. Cecil H. and Ida Green Distinguished Chair Professor Director, Center for Systems Biology Department of Biological Sciences The University of Texas at Dallas -- ------------------------------------- Hao Li, Professor Dept. of Biochemistry and Biophysics Director, Larry L. Hillblom Center for the Biology of Aging University of California, San Francisco 1700 4th Street, Room 403A, Box 2542 San Francisco, CA 94143-2542 For direct delivery: Use Zip code 94158 office phone: (415)502-8187 Fax: (415)514-2617 email: haoli(a)genome.ucsf.edu http://mobydick.ucsf.edu/~haoli/ ------------------------------------

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[Compbio-allhands] Vertex Fellow Program
by Andrej Sali 09 Mar '16

09 Mar '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94158-2330, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Assistant: Ms. Hilary Mahon, hilary(a)salilab.org, Tel +1 (415)514-4228; Lab +1 (415) 514-4233, 4258 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Fwd: Vertex Fellows Program
by Brian Shoichet 04 Mar '16

04 Mar '16

Might be an interesting opportunity, even for faculty. Brian Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Jonathan Moore" <jonathan_moore(a)vrtx.com> Date: Mar 4, 2016 6:10 AM Subject: Vertex Fellows Program To: "shoichet(a)cgl.ucsf.edu" <shoichet(a)cgl.ucsf.edu> Cc: Dear Brian, I hope all is well. I'm writing to tell you about a new Fellowship program we're launching at Vertex, and to ask for your help with identifying great candidates. The new Vertex Fellowship is intended to attract some of the most talented scientists and physicians to join Vertex for one year of immersive learning about the science of drug discovery and, in the process, expose us to diverse and innovative ways of thinking. Each Vertex Fellow will be embedded with a drug discovery project team based on their interests and our needs. In addition, we will provide Fellows with didactic multi-disciplinary training on the science of drug discovery. The program is intentionally short (one year) so it augments rather than replaces traditional postdoctoral training. David Altshuler (CSO) will personally oversee the program together with our most senior scientists (Principal Research Fellows). We expect to take on 3 - 6 Vertex Fellows across our sites in the Fall of 2016. We will provide career advice and mentorship to help the fellows on their way to a successful career in biomedical science. I am asking for your help with identifying potential Fellows who would be excited about such an opportunity. Fellows could be finishing a PhD, MD or joint program, or completing clinical training. We will also consider faculty who have a sabbatical and would be interested in the experience. (Kit Parker, a faculty member at Harvard, is currently spending a sabbatical at Vertex.) In short, Vertex Fellows will: · Learn about drug discovery at an innovative biotechnology company · Help patients by contributing to transformative medicines · Advance a scientific idea rapidly and effectively in a team-based environment · Receive mentorship from scientific, medical and business leaders · Join a community of Fellows that will span Vertex and academia · Accelerate their careers by learning new skills in a different setting *Do you know anyone who might be a good fit?* I'm attaching a 1-page flyer with more information. Please let me know what questions or feedback you have about the program. I’d be particularly grateful if you would pass this along to any potential Fellows whom you think might be interested. Thanks for your help, Jon Jonathan M. Moore Principal Research Fellow and Vice President Exploratory Biochemistry Vertex Pharmaceuticals Incorporated 50 Northern Avenue Boston, MA 02210 Phone: 617-341-6444 This email message and any attachments are confidential and intended for use by the addressee(s) only. If you are not the intended recipient, please notify me immediately by replying to this message, and destroy all copies of this message and any attachments. Thank you.

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[Compbio-allhands] 3/10/16 Seminar with Tuuli Lappalainen
by Flowers, Nicole 04 Mar '16

04 Mar '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Tuuli Lappalainen New York Genome Center & Columbia University Functional variation in the human genome: lessons from the transcriptome March 10, 2016 T. Friedrich, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 3/3/16 Seminar with Carrie Partch
by Flowers, Nicole 26 Feb '16

26 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Carrie Partch UC Santa Cruz Dissecting the molecular basis for circadian timekeeping March 3, 2016 D. Fujimori, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Recommendations for computational chemist position
by Jacobson, Matt 24 Feb '16

24 Feb '16

- Matt Begin forwarded message: From: David Weinberg <david.weinberg(a)ucsf.edu<mailto:david.weinberg@ucsf.edu>> Subject: Fwd: Recommendations for computational chemist position Date: February 24, 2016 at 2:12:57 PM PST To: Brian Shoichet <bshoichet(a)gmail.com<mailto:bshoichet@gmail.com>>, Matthew Jacobson <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt and Brian, Jaime suggested that you guys might know someone that's a good fit for this position at Moderna Therapeutics (with whom I collaborate). See below for the details and let me know if you want me to pass on anyone's name. Best, David ------------------------------- David Weinberg, PhD UCSF Faculty Fellow University of California, San Francisco Department of Cellular and Molecular Pharmacology Office: Genentech Hall S572F // Lab: Genentech Hall S576 Phone: (415) 514-9723 // Fax: (415) 514-4112 david.weinberg(a)ucsf.edu<mailto:david.weinberg@ucsf.edu> // deweinberg(a)gmail.com<mailto:deweinberg@gmail.com> ---------- Forwarded message ---------- From: Iain McFadyen <Iain.McFadyen(a)modernatx.com<mailto:Iain.McFadyen@modernatx.com>> Date: Wed, Feb 24, 2016 at 12:10 PM Subject: Recommendations for computational chemist position To: Iain McFadyen <Iain.McFadyen(a)modernatx.com<mailto:Iain.McFadyen@modernatx.com>> I’m looking for a talented and creative computational chemist to work on structure-based design of modified nucleotides, cap analogs, tail modifications, and lipid components in collaboration with our chemistry group. If you know of someone that might fit that description, please let me know! Thanks, and hope you don’t mind this random question – I’m trying to cast as wide a net as possible. Iain P Please consider the environment before printing this email Confidentiality notice and disclaimer: The information in this message and any attachments is intended for the exclusive use of the addressee(s), is confidential and may be privileged or otherwise protected from disclosure. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, of any such information by persons or entities other than the intended addressee(s) is prohibited. If you have received this message in error and are not the intended addressee, please notify the sender immediately and delete this message and any attachments from your system without reading or disclosing them. If you are not the intended addressee, be advised that any use of the information in this message and any attachment is prohibited and may be unlawful, and you must not copy this message or attachment or disclose the contents to any other person.

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[Compbio-allhands] Fwd: Postdoctoral position on integrating structural biology with big data to engineer next generation vaccines
by Andrej Sali 20 Feb '16

20 Feb '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Jens Meiler" <jens(a)meilerlab.org> > Subject: Postdoctoral position on integrating structural biology with big data to engineer next generation vaccines > Date: February 20, 2016 at 12:52:56 PM PST > To: "James Crowe" <james.crowe(a)vanderbilt.edu> > > Please distribute widely: > > The laboratories of James E. Crowe and Jens Meiler are looking immediately > for outstanding postdoctoral candidates that will join a team of graduate > and post-graduate researchers co-advised by both mentors. The candidates > would work to integrate structural biology with big data to engineer next > generation vaccines targeting influenza, HIV, Ebola, or Marburg viruses. The > project involves computational design of broadly neutralizing antibodies, > computational engineering of vaccine candidates, and experimental structural > and functional characterization of these. Skills that are a plus, but not > all would be required, include programming/scripting, experimental > structural biology (X-ray, NMR, EM, ...), Rosetta modeling, immunology. If > interested, please submit a CV and arrange three letters of reference sent > to jens(a)meilerlab.org and james.crowe(a)vanderbilt.edu. > > ==================================================================== > > Jens Meiler, Ph.D. > Chancellor Faculty Fellow > Associate Professor > Vanderbilt University > Departments of Chemistry, Pharmacology, and Biomedical Informatics Center > for Structural Biology, Institute for Chemical Biology > > ==================================================================== > > office: MRBIII, Room 5144 B, 465 21st Ave South, Nashville, TN 37240 > mail : 7330 Stevenson Center, Station B 351822, Nashville, TN 37235 > e-mail: jens(a)meilerlab.org > WWW: www.meilerlab.org > Twitter: https://twitter.com/MeilerLab > Phone: +1 (615) 936-5662 > Fax: +1 (615) 936-2211 > Assistant: h.darling(a)vanderbilt.edu > > ==================================================================== > > >

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[Compbio-allhands] 2/25/16 Seminar with Michael Rosen
by Flowers, Nicole 19 Feb '16

19 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Michael Rosen UT Southwestern Physical Mechanisms of Cell Organization on Micron Length Scales February 25, 2016 J. Lobel, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Post Doc @ Imperial - Developing a structure-based database of genetic variants
by Andrej Sali 15 Feb '16

15 Feb '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Sternberg, Michael J E" <m.sternberg(a)imperial.ac.uk> > Subject: Post Doc @ Imperial - Developing a structure-based database of genetic variants > Date: February 15, 2016 at 1:58:05 AM PST > To: Undisclosed recipients:; > > I would be grateful if you would forward to suitable finishing PhD students and postdocs > Many thanks Mike > ------------------------------------- > > > Research Associate in Bioinformatics > Developing > > Imperial College, South Kensington Campus > Department of Life Sciences/Faculty of Natural Sciences > Salary £33,860-£42,830 per annum > > Applications are invited for a Research Associate position to join the Structural Bioinformatics Group, within the Department of Life Sciences based at the South Kensington Campus. The post holder will work as a member of a small team developing the software for the PhyreRisk portal which will provide a web portal to deliver to the community a resource relating human genetic variation, disease, protein structure and biological pathways. > The post holder will be responsible for developing the PhyreRisk database and provide support to users of Phyre Risk. You will collaborate closely with other members of the team modelling protein structure and you will be involved in disseminating PhyreRisk to the community. You will also be expected to apply the portal to specific problems including those at the Institute of Cancer Research in London. In addition you also assist with the teaching and the administration of research groups. > > You must have a PhD (or equivalent) involving substantial development of software to study biological systems at the genetic or molecular level. You will have proven programming experience that results in the development of a substantive and robust algorithm, web-site or database tackling a problem in protein modelling or the analysis of genetic variants. Extensive knowledge of either modelling protein structure or the analysis of genetic variants together with extensive experience of developing either web site using JavaScript/HTML (or equivalent) or an SQL (or equivalent) database for use by the bioscience and biomedical communities are essential. Understanding of the application of statistics in bioinformatics is also essential. You must have the ability to express scientific concepts verbally and in writing, especially those in bioinformatics, precisely and clearly. Ability to develop high-level code to a professional standard of robustness and clarity is also essential. Ability to identify the technical and scientific steps that need to be accomplished to develop novel and complex bioinformatics software with minimal supervision is highly desirable. > You must have excellent verbal and written communication skills, and be able to write clearly and succinctly for publication. You must be able to relate well with others, form positive relationships with a wide range of people and to work as part of a team, as well as independently and be able to prioritise in respond to deadlines. You must have a pro-active attitude in the planning of research work, and have a creative approach to problem-solving. > This is a full time position, funded by the Welcome Trust for up to three years. > Closing Date : 14 March 2016 (midnight GMT) > > How To Apply: Our preferred method of application is online via > https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf… <https://www4.ad.ic.ac.uk/OA_HTML/OA.jsp?page=/oracle/apps/irc/candidateSelf…>. > Should you have any queries please contact: Professor Michael Sternberg by email:m.sternberg@imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> Alternatively, if you are unable to apply online, please contact dols.recruitment(a)imperial.ac.uk <mailto:dols.recruitment@imperial.ac.uk> by email to request an application form > > > > ******************************************** > Professor Michael J E Sternberg > Director Centre for Integrative Systems Biology and Bioinformatics (CISBIO) > Room 306 - Sir Ernst Chain Building > Department of Life Sciences > Imperial College London, London SW7 2AZ,UK > m.sternberg(a)imperial.ac.uk <mailto:m.sternberg@imperial.ac.uk> > http://www3.imperial.ac.uk/cisbio <http://www3.imperial.ac.uk/cisbio> (CISBIO) > www.sbg.bio.imperial.ac.uk <http://www.sbg.bio.imperial.ac.uk/> (Group's research) > > Tel +44 (0)20 7594 5212 > ****************************************************************************

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[Compbio-allhands] 2/18/16 Seminar with Erin O'Shea
by Flowers, Nicole 12 Feb '16

12 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Erin O'Shea Harvard Timekeeping by a Three Protein Circadian Clock February 18, 2016 J. Weissman, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 2/11/16 Seminar with Alice Ting
by Flowers, Nicole 05 Feb '16

05 Feb '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Alice Ting MIT Spatially-Resolved Proteomic Mapping of Living Cells Reveals New Proteins and Functions in the Mitochondria and Neuronal Synapse February 11, 2016 J Perez Bermejo, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 2/4/16 Seminar with Taekjip Ha
by Flowers, Nicole 29 Jan '16

29 Jan '16

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Taekjip Ha University of Illinois at Urbana-Champaign Surprising Physics of DNA on the Genome Scale February 4, 2016 T. Lee, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 1/28/16 NO BBC SEMINAR
by Flowers, Nicole 28 Jan '16

28 Jan '16

There is no BBC Seminar today, January 28, 2016. Thank you, Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Job opening for Genetic Bioinformatics at NIDA
by Tom Ferrin 27 Jan '16

27 Jan '16

-------- Forwarded Message -------- Subject: Job opening for Genetic Bioinformatics at NIDA Date: Wed, 27 Jan 2016 17:45:58 +0000 From: Pollock, Jonathan (NIH/NIDA) [E] <jpollock(a)nida.nih.gov> To: tef(a)cgl.ucsf.edu <tef(a)cgl.ucsf.edu> Dear Colleague: Dear Dr. Ferrin, I wish to bring to your attention a job opening in my branch, The Genetics, Epigenetics, and Developmental Neuroscience Branch, in the Division of Neuroscience and Behavior at NIDA for the position of program director in Genetic Bioinformatics. The posting on USAjobs became active on 1/27/16 and will close 2/5/16. Here are links to the vacancy announcement: DE: https://www.usajobs.gov/GetJob/ViewDetails/427694600. The DE vacancy is open to all US Citizens so applicants who currently do not work for the Federal government should apply to this announcement. MP: _https://www.usajobs.gov/GetJob/ViewDetails/427699100. _The Merit Promotion vacancy is for those candidates who currently work or are former Federal employees. The announcement is open only to US Citizens. Underrepresented minorities are encouraged to apply. The position is at the GS-14 level ($108,887 to $141,555) and is located at NIDA headquarters in Rockville, MD. The ideal candidate will have a doctorate in neuroscience, molecular biology, or genetics/epigenetics with research experience in bioinformatics and genetics/epigenetics. The successful candidate can have a huge impact on public health, on the direction of science and will have the opportunity to write papers that analyze existing datasets. Much of the health burden stems from substance abuse and addiction. Specifically the duties of the job are to * provide technical leadership and guidance in bioinformatics of human genome and epigenomic data. * plan and direct research program activities in the area of associated data science * analyze trends and data to assess the adequacy of research being conducted and proposed epigenetics and genetics of addiction and drug abuse. * identify gaps in existing scientific research. * identify advances and developments in bioinformatics, research design and statistical genetics. * propose a comprehensive and cohesive research plan outlining the direction and long-term goals to be accomplished. * analyze the scientific merit of current and projected research programs. * identify and recommend the program direction of new research. * assess the scientific progress of research or clinical programs to ensure that objectives are being attained. * develop new analytical tools to analyze data from established data infrastructure. * lead program and researchers in managing and analyzing new and emerging data resources. * provide advice to grantees/contractors during preparation of applications/proposals. * advise and evaluate grants/awards, cooperative agreements of biomedical research in genetics/epigenetics. * recommend and distribute research funding for new research initiatives/efforts. * Initiate appropriate action relative to the grantee/contractor when research progress is inadequate. * administer unsolicited grant/contract proposals and provide support regarding funding options and areas of program emphasis. * establish or participate in panels to review research proposals or reports, including the criteria and standards for the panel to follow. * evaluate the technical and scientific merit of funding applications and proposals being submitted for approval. * examine the technical and scientific merit of research proposals. * manage research fund distribution amongst competing interests within an organization. I would appreciate your assistance in this search process and welcome your application or nomination of applicants whom you feel could provide the leadership and scientific excellence required of this position. I would appreciate your forwarding this announcement to scientists who may be well qualified for the position. I would be particularly interested in your calling this employment opportunity to the attention of well-qualified applicants from traditionally under-represented groups. The announcement is open only to US Citizens Feel free to contact me, Jonathan D. Pollock, Ph.D., Chief, Genetics, Epigenetics, and Developmental Neuroscience Branch with any questions regarding this announcement. Sincerely, Jonathan D. Pollock, Ph.D. Jonathan D. Pollock, Ph.D. Chief Genetics, Epigenetics, and Developmental Neuroscience Branch Division of Neuroscience and Behavior National Institute on Drug Abuse, NIH 6001 Executive Blvd, Rm. 4267 Bethesda, MD 20892 Tel. 301-435-1309 Email. jpollock(a)mail.nih.gov <mailto:jpollock@mail.nih.gov> Skype: Dogmacentral1

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[Compbio-allhands] Fwd: Job opening for Genetic Bioinformatics at NIDA
by Andrej Sali 27 Jan '16

27 Jan '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Associate Dean for Research, School of Pharmacy Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552, Byers Hall Room 503B 1700 4th Street, San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Pollock, Jonathan (NIH/NIDA) [E]" <jpollock(a)nida.nih.gov> > Subject: Job opening for Genetic Bioinformatics at NIDA > Date: January 27, 2016 at 9:42:22 AM PST > To: "sali(a)salilab.org" <sali(a)salilab.org> > > > > > Dear Dr. Sali, > > I wish to bring to your attention a job opening in my branch, The Genetics, Epigenetics, and Developmental Neuroscience Branch, in the Division of Neuroscience and Behavior at NIDA for the position of program director in Genetic Bioinformatics. The posting on USAjobs became active on 1/27/16 and will close 2/5/16. Here are links to the vacancy announcement: > > DE: https://www.usajobs.gov/GetJob/ViewDetails/427694600 <https://www.usajobs.gov/GetJob/ViewDetails/427694600>. The DE vacancy is open to all US Citizens so applicants who currently do not work for the Federal government should apply to this announcement. > > MP: https://www.usajobs.gov/GetJob/ViewDetails/427699100 <https://www.usajobs.gov/GetJob/ViewDetails/427699100>. The Merit Promotion vacancy is for those candidates who currently work or are former Federal employees. > > The announcement is open only to US Citizens. Underrepresented minorities are encouraged to apply. > > The position is at the GS-14 level ($108,887 to $141,555) and is located at NIDA headquarters in Rockville, MD. The ideal candidate will have a doctorate in neuroscience, molecular biology, or genetics/epigenetics with research experience in bioinformatics and genetics/epigenetics. The successful candidate can have a huge impact on public health, on the direction of science and will have the opportunity to write papers that analyze existing datasets. Much of the health burden stems from substance abuse and addiction. > > Specifically the duties of the job are to > > provide technical leadership and guidance in bioinformatics of human genome and epigenomic data. > plan and direct research program activities in the area of associated data science > analyze trends and data to assess the adequacy of research being conducted and proposed epigenetics and genetics of addiction and drug abuse. > identify gaps in existing scientific research. > identify advances and developments in bioinformatics, research design and statistical genetics. > propose a comprehensive and cohesive research plan outlining the direction and long-term goals to be accomplished. > analyze the scientific merit of current and projected research programs. > identify and recommend the program direction of new research. > assess the scientific progress of research or clinical programs to ensure that objectives are being attained. > develop new analytical tools to analyze data from established data infrastructure. > lead program and researchers in managing and analyzing new and emerging data resources. > provide advice to grantees/contractors during preparation of applications/proposals. > advise and evaluate grants/awards, cooperative agreements of biomedical research in genetics/epigenetics. > recommend and distribute research funding for new research initiatives/efforts. > Initiate appropriate action relative to the grantee/contractor when research progress is inadequate. > administer unsolicited grant/contract proposals and provide support regarding funding options and areas of program emphasis. > establish or participate in panels to review research proposals or reports, including the criteria and standards for the panel to follow. > evaluate the technical and scientific merit of funding applications and proposals being submitted for approval. > examine the technical and scientific merit of research proposals. > manage research fund distribution amongst competing interests within an organization. > > I would appreciate your assistance in this search process and welcome your application or nomination of applicants whom you feel could provide the leadership and scientific excellence required of this position. I would appreciate your forwarding this announcement to scientists who may be well qualified for the position. I would be particularly interested in your calling this employment opportunity to the attention of well-qualified applicants from traditionally under-represented groups. > > The announcement is open only to US Citizens > > > Feel free to contact me, Jonathan D. Pollock, Ph.D., Chief, Genetics, Epigenetics, and Developmental Neuroscience Branch with any questions regarding this announcement. > > > Sincerely, > > > > Jonathan D. Pollock, Ph.D. > > > Jonathan D. Pollock, Ph.D. > Chief > Genetics, Epigenetics, and Developmental Neuroscience Branch > Division of Neuroscience and Behavior > National Institute on Drug Abuse, NIH > 6001 Executive Blvd, Rm. 4267 > Bethesda, MD 20892 > Tel. 301-435-1309 > Email. jpollock(a)mail.nih.gov <mailto:jpollock@mail.nih.gov> > Skype: Dogmacentral1

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[Compbio-allhands] computational jobs at Third Rock startup
by Jacobson, Matt 25 Jan '16

25 Jan '16

Job descriptions below. I have been working with Third Rock to start this company, which will focus exclusively on allosteric drug discovery. The company has not been officially announced and these job descriptions are preliminary, but they are looking to identify good candidates in anticipation of a rapid launch. Anyone interested can send CV/resume to the CSO, Mark Murcko (mark.murcko(a)gmail.com<mailto:mark.murcko@gmail.com>) or to me (matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>). Feel free to forward. Thanks, Matt ============================ POSITION #1 Relay Therapeutics is seeking a highly motivated computational chemist to join our rapidly growing team. This individual will utilize cutting edge computational methods, in conjunction with information generated by a variety of structural and biophysical techniques, to design novel therapeutics targeted to allosteric sites. In this role, the ideal candidate will work as part of a multidisciplinary team to integrate computational and experimental insights and drive drug discovery. Responsibilities * Carry out analyses that combine computational and experimental data to develop testable hypotheses that drive drug discovery programs * Collaborate with scientists throughout the company as well as academic founders and other external advisors to maximize the impact of computational efforts on projects * Work collaboratively with external computational groups to develop and refine new computational methods * Ensure effective communication of computational results across departments and teams * Develop new approaches to streamline and enhance computational workflows [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] Preferred Qualifications * Ph.D. in Computational Chemistry, Computational Biology, Biophysics, or a related discipline * 1 to 5 years of industrial or postdoctoral experience * Demonstrated expertise applying wide variety of modern computational chemistry methods to drug discovery * Demonstrated expertise in structure-based drug design * In depth knowledge of molecular dynamics and its application to drug discovery * Facility working in a Unix/Linux environment * Ability to program in at least 1 modern scripting language (e.g. Python) * Strong interpersonal and communications skills * Ability to conduct independent research ========================================= POSITION #2 Relay Therapeutics seeks a skilled, creative scientific software developer to develop novel computational workflows to streamline our drug discovery efforts. The ideal candidate will combine scientific knowledge and full-stack web development skills to design and develop user interfaces as well as back-end infrastructure. Responsibilities * Work collaboratively with scientists to understand needs for data flow, access and analysis * Develop scripts and applications to streamline scientific workflows * Develop web-based user interfaces to support data input and analysis * Utilize commercial, as well as internally developed software to design and maintain an infrastructure to facilitate decision making in drug discovery Preferred Qualifications * BA or BS in Chemistry, Biology, Physics or a related discipline * 2 to 5 years experience developing software to support pharmaceutical research * Demonstrated knowledge of Cheminformatics * Demonstrated ability to program in Python and JavaScript * Experience with at least one modern JavaScript framework (e.g. Angular, React, ExtJS) * Expertise with databases and SQL * Experience programming with commercial or open source cheminformatics toolkits (e.g. OEChem, RDKit, Open Babel) * - Matt

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[Compbio-allhands] Fwd: position for biophysicist at Biodesy
by Andrej Sali 22 Jan '16

22 Jan '16

fyi > Begin forwarded message: > > From: Joshua Salafsky <joshua.salafsky(a)biodesy.com> > Subject: position for biophysicist at Biodesy > Date: January 22, 2016 at 4:35:19 PM PST > To: Andrej Sali <sali(a)salilab.org>, "Shoichet, Brian" <bshoichet(a)gmail.com> > > Hi guys, > In case you happen to know of anyone suitable, we are looking for an experimental with some experience with computational structural biology (please see attached). > > Thanks, > Josh > > Joshua Salafsky, PhD > > Founder & Chief Scientific Officer > Biodesy, Inc. > 384 Oyster Point Boulevard, #8 > South San Francisco, CA 94080 > > (415) 640-6210 > joshua.salafsky(a)biodesy.com <mailto:joshua.salafsky@biodesy.com>

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[Compbio-allhands] Fwd: 1/26/16 Seminar with Aled Edwards
by Jacobson, Matt 20 Jan '16

20 Jan '16

- Matt Begin forwarded message: From: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> Subject: 1/26/16 Seminar with Aled Edwards Date: January 20, 2016 at 4:07:52 PM PST To: <PSPGFACULTY(a)LISTSRV.UCSF.EDU<mailto:PSPGFACULTY@LISTSRV.UCSF.EDU>> Reply-To: "Flowers, Nicole" <Nicole.Flowers(a)UCSF.EDU<mailto:Nicole.Flowers@UCSF.EDU>> PSPG Graduate Program/CERSI Seminar Series Pharmaceutical Sciences & Pharmacogenomics Center for Excellence in Regulatory Science & Innovation Tuesdays, 12 Noon Rock Hall Auditorium Simulcast to Parnassus Campus N225 Aled Edwards University of Toronto Open source discovery of new drug targets using chemical probes January 26, 2016 B. Shoichet, Host Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546 ________________________________ Use this link to unsubscribe<http://listsrv.ucsf.edu/cgi-bin/wa?TICKET=NzM2MDEzIG1hdHQuamFjb2Jzb25AVUNTR…> from this mailing list.

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[Compbio-allhands] PETER KOLLMAN LECTURESHIP- JANUARY 21, 2016
by Flowers, Nicole 20 Jan '16

20 Jan '16

Michael Gilson UC San Diego The Physical Basis of Computer-Aided Drug Design Thursday, January 21, 2016 12:00 PM PETER A. KOLLMAN LECTURESHIP Genentech Hall Byers Auditorium UCSF Mission Bay Campus Simulcast to Parnassus Campus S-161 Webcast: http://lecture.ucsf.edu/ets/Play/a4adc34fa08b46fa9388e9e0aab8f5f41d Reception in Byers Hall 3rd Floor Lounge at 3:30 pm. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Postdoc Position in NMR
by Andrej Sali 13 Jan '16

13 Jan '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: pau bernado <pau.bernado(a)cbs.cnrs.fr> > Subject: Postdoc Position in NMR > Date: January 13, 2016 at 9:47:54 AM GMT+1 > To: pau bernado <pau.bernado(a)cbs.cnrs.fr>, Nathalie Sibille <nathalie.sibille(a)cbs.cnrs.fr> > > Dear Colleague, > > Our group is opening a two-year postdoc position in NMR to work at the Centre de Biochimie Structurale (CBS) in Montpellier. Please, spread this information to students or postdocs that could be interested. > Candidates should have a strong background in solution NMR. Expertise in protein expression and purification, or computational approaches is highly recommended. The project aims at studying Intrinsically Disordered Proteins related with cell signaling and neurodegenerative diseases. Find attached a more detailed description of the position. > > Thanks a lot for your collaboration and best regards > > Pau Bernadó > > > >

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[Compbio-allhands] Fwd: Senior level faculty search in computational biology at UMass Amherst
by Andrej Sali 12 Jan '16

12 Jan '16

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: Lila Gierasch <gierasch(a)biochem.umass.edu> > Subject: Senior level faculty search in computational biology at UMass Amherst > Date: January 12, 2016 at 11:39:21 PM GMT+1 > To: Ken Dill <dill(a)maxwell.compbio.ucsf.edu>, D Thirumalai <thirum(a)umd.edu>, Angel Garcia <angel(a)rpi.edu>, Vijay Pande <pande(a)stanford.edu>, Rohit Pappu <pappu(a)wustl.edu>, Jose Onuchic <jonuchic(a)rice.edu>, George Makhatadze <makhag(a)rpi.edu>, case <case(a)biomaps.rutgers.edu>, brookscl(a)umich.edu, pwolynes(a)ucsd.edu, brunger(a)stanford.edu, Andrej Sali <sali(a)salilab.org>, David Baker <dabaker(a)u.washington.edu>, Oliver Brock <oliver.brock(a)tu-berlin.de>, George Rose <grose(a)jhu.edu>, Dave Thirumalai <thirum(a)umd.edu>, Ruth Nussinov <ruthn(a)ncifcrf.gov>, "David A. Agard" <agard(a)msg.ucsf.edu>, Vince Hilser <hilser(a)jhu.edu>, Chris Sander C <sanderc(a)mskcc.org>, eugene(a)belok.harvard.edu, palsson(a)ucsd.edu, ronlevy(a)temple.edu, chan(a)arrhenius.med.utoronto.ca, sali(a)salilab.org, Arnie Hagler <athagler(a)gmail.com>, bh6(a)columbia.edu, Woody Sherman <woody.sherman(a)gmail.com> > > Hi friends- > > I wanted to let you know about a faculty search at UMass Amherst in computational biology and to ask your help in spreading the word about this exciting opportunity. Within the broad area of computational biology, we would be delighted to have applicants from any of a wide range of topics: including molecular-level modeling, such as protein-protein interactions, docking of small molecules, simulations of dynamics and conformational change; analysis of large data sets and –omic results; or modeling of systems and networks. This search has been launched under the aegis of our new Institute for Applied Life Sciences (IALS), and we seek a mid-career scientist whose star is rising and whose research is directed towards therapeutic goals, such as target discovery. In addition, we want to attract someone who enjoys collaboration and has synergistic research interests with IALS scientists in areas like protein homeostasis, cancer, immunology, drug delivery, and more. Interested candidates can take a look at the IALS faculty research themes at: https://www.umass.edu/ials/ <https://www.umass.edu/ials/> > It’s a very exciting time at UMass Amherst, and we are looking for a number of new hires in addition to the computational biologist (see the attached ad). The state has invested in the campus to the tune of $140M to start IALS, and many new core facilities have been created and others enhanced (see https://www.umass.edu/ials/core-facilities <https://www.umass.edu/ials/core-facilities>). For a computational biologist, it is also exciting that we are establishing a new College of Information and Computer Sciences (www.cics.umass.edu <http://www.cics.umass.edu/>), and the campus is a partner in the Green High Performance Computing Center located in nearby Holyoke, MA (www.mghpcc.org/) > > Please help spread the word. The Amherst area is a great place to live, the Five-Colleges Inc collaboration is a super aspect, and UMass Amherst is truly blossoming. The search is now open, and consideration of candidates will continue until we fill the position. > > Best, > > Lila > > > > > > Lila M. Gierasch > Distinguished Professor > Depts. of Biochemistry & Molecular Biology and Chemistry > Life Sciences Laboratories Room N331 > 240 Thatcher Way > University of Massachusetts, Amherst > Amherst, Massachusetts 01003-9364 > Tel 413-545-6094 > Fax 413-545-1289 > email: gierasch(a)biochem.umass.edu <mailto:gierasch@biochem.umass.edu> > http://www.biochem.umass.edu/biochem/gierasch/index.html <http://www.biochem.umass.edu/biochem/gierasch/index.html> > http://people.chem.umass.edu/gieraschlab > > >

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[Compbio-allhands] Fwd: job opening at Novartis Emeryville
by Andrej Sali 11 Jan '16

11 Jan '16

Sent from my iPhone Begin forwarded message: > From: Dave Barkan <davebarkan(a)gmail.com> > Date: January 11, 2016 at 5:07:08 PM GMT+1 > To: Andrej Sali <sali(a)salilab.org> > Subject: job opening at Novartis Emeryville > > Hey Andrej! > > Hope things are going well. We have an opening for an entry-level Investigator position in our Infectious Diseases group in Emeryville. Talented post-docs from bioinformatics-focused labs at UCSF, or newly minted PhD graduate students, would be good candidates. Could you please circulate the following link? > > http://jobs.brassring.com/1033/ASP/TG/cim_jobdetail.asp?partnerid=13617&sit… > > Thanks! > Dave

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[Compbio-allhands] Fwd: LabEx LERMIT - "New Group Leader" Call
by Brian Shoichet 11 Jan '16

11 Jan '16

FYI Brian Shoichet, Professor Dept. of Pharmaceutical Chemistry, UCSF by courtesy: Faculty of Pharmacy & OICR, UofT sent from my phone. ---------- Forwarded message ---------- From: "Aurelie Lando" <aurelie.lando(a)u-psud.fr> Date: Jan 11, 2016 2:04 AM Subject: LabEx LERMIT - "New Group Leader" Call To: "atartar" <andre.tartar(a)univ-lille2.fr>, "Ralph Schermuly" < Ralph.Schermuly(a)innere.med.uni-giessen.de>, "Francois Ballet" < fballet(a)medicen.org>, "Lehr Claus-Michael" <lehr(a)mx.uni-saarland.de>, "Harding, Sian E" <sian.harding(a)imperial.ac.uk>, "Houslay, Miles" < miles.houslay(a)kcl.ac.uk>, "Kevin Harrington" <Kevin.Harrington(a)icr.ac.uk>, "Beat Ernst" <beat.ernst(a)unibas.ch>, "michel.bouvier(a)umontreal.ca" < michel.bouvier(a)umontreal.ca>, "jlederer(a)umaryland.edu" < jlederer(a)umaryland.edu>, "lederer(a)umbi.umd.edu" <lederer(a)umbi.umd.edu>, "Ulf Lindahl" <ulf.lindahl(a)imbim.uu.se>, "Storm, G." <G.Storm(a)uu.nl>, "Mark Sansom" <mark.sansom(a)bioch.ox.ac.uk>, "Gunda Georg" <georg(a)umn.edu>, " vera.regitz-zagrosek(a)charite.de" <vera.regitz-zagrosek(a)charite.de>, " carlo.croce(a)osumc.edu" <carlo.croce(a)osumc.edu>, "Meijer Manros" < meijer(a)manros-therapeutics.com>, "stephen.archer(a)queensu.ca" < stephen.archer(a)queensu.ca>, "Hossam Haick" <hhossam(a)tx.technion.ac.il>, "Sam Gellman" <gellman(a)chem.wisc.edu>, "Juliano, Rudolph L" < rudy_juliano(a)med.unc.edu>, "Kungl, Andreas (andreas.kungl(a)uni-graz.at)" < andreas.kungl(a)uni-graz.at>, "Tom Blundell" <tom(a)cryst.bioc.cam.ac.uk>, "Uchegbu, Ijeoma" <ijeoma.uchegbu(a)ucl.ac.uk>, "Brian Shoichet" < bshoichet(a)gmail.com>, "Maria Jose Alonso" <mariaj.alonso(a)usc.es>, " jsamitier(a)ub.edu" <jsamitier(a)ub.edu> Cc: "rodolphe.fischmeister(a)inserm.fr" <rodolphe.fischmeister(a)inserm.fr>, " david.bonnaffe(a)u-psud.fr" <david.bonnaffe(a)u-psud.fr> *New Group Leader Call 2016 - LabEx LERMIT * The Laboratory of Excellence in Research on Medication and Innovative Therapeutics (LabEx LERMIT) is launching an international call for an outstanding new group leader willing to establish an independent research group within one of the LERMIT partner laboratories. The content of this call is attached. The dead-line for application is May 17th, 2016. Thank you to spread widely this offer among your contacts and especially junior scientists who may be interested in establishing their research activity in France. Rodolphe Fischmeister Coordinator David Bonnaffé Vice-Coordinator P/O Aurélie Lando -- Dr.Aurélie Lando Administrative Project Manager LabEx LERMITwww.labex-lermit.fr Faculté de Pharmacie Tour D1 1er étage Université Paris-Sud 5 Rue Jean-Baptiste Clément 92296 Châtenay-Malabry Cedexaurelie.lando(a)u-psud.fr tel : +33 (0)1 46 83 52 46

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[Compbio-allhands] Fwd: Help with a post doc??
by Andrej Sali 23 Dec '15

23 Dec '15

Sent from my iPhone Begin forwarded message: > From: John Aitchison <John.Aitchison(a)systemsbiology.org> > Date: December 23, 2015 at 3:24:38 PM PST > To: John Aitchison <john.aitchison(a)cidresearch.org> > Subject: Help with a post doc?? > > Hi Friends, > I am looking for a post-doc to pick up on a great project involving systems biology and dengue virus. The ideal person would have experience, be interested in, systems cell biology in the context of infectious disease. I would greatly appreciate passing this on to any exceptional people you think might be interested. > Thank you, and happy holidays, > John > > John Aitchison, PhD > Professor > Institute for Systems Biology >

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[Compbio-allhands] Fwd: Postdoc merging structure-based drug design with physiologically-based pharmacokinetic simulations
by Jacobson, Matt 11 Dec '15

11 Dec '15

- Matt Begin forwarded message: From: "Martin, Eric" <eric.martin(a)novartis.com<mailto:eric.martin@novartis.com>> Subject: Postdoc merging structure-based drug design with physiologically-based pharmacokinetic simulations Date: December 11, 2015 at 4:36:47 PM PST To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, I recently obtained funding to extend the work we have been doing in adapting physiologically-based pharmacokinetic simulations to drug lead optimization. Given your groups work in both structure-based virtual screening and on PK parameters like membrane permeability, serum albumin binding, PgP efflux, and brain exposure, I think your students would be very well prepared to take on this challenging interdisciplinary postdoctoral project. I would appreciate your passing this opportunity along to any appropriate students. Best wishes, Eric Rational Bioavailability Design using Physiologically-Based Pharmacokinetics Simulations This computational postdoctoral project is at the interface of several scientific disciplines: chemistry, enzyme kinetics, pharmacokinetics, mathematical simulations, and statistics. Structure-based drug design (SBDD) is the main computational tool for improving binding affinity during lead optimization (LO), but does not address whole animal efficacy. We have recently developed methodology to perform reliable physiologically-based pharmacokinetic (PBPK) simulations of absorption, distribution, metabolism and elimination (ADME) not just for a few, well studied, late-stage compounds, but for entire medchem series, using only inputs computed from chemical structure. These whole-animal simulations only require about 15 rat PK studies for training, typically available early enough to impact LO. We analyze thousands of these simulations with partial least squares regression (PLS) based global sensitivity analysis to identify which few of perhaps a dozen compound properties dominate improved bioavailability across each entire series, as well as for each specific compound. Furthermore, the PLS function provides a very good approximation of the full PBPK simulation for that series. While this work has extended PBPK modeling to LO, it does not yet suggest specific compounds to synthesize, and does not account for how whole-animal ADME interacts with molecular binding kinetics to determine target occupancy over time, and therefore efficacy. We now aim to integrate interactive SBDD and in silico compound evolution with multi-objective scoring functions that include both affinity and the PLS approximation of exposure, and to incorporate binding kinetics into the full PBPK simulations. This multi-scale systems biology approach to drug design would complete a path from SBDD, through binding-kinetics enabled PBPK and pharmacodynamics, enabling SBDD not just of ligand binding, but of in vivo efficacy. The goal is ambitious, yet the risks are minimized because the components are established methods, and we can draw on internal Novartis experts in all the required disciplines. Eric Martin Director, Computational Chemistry Novartis Institutes for BioMedical Research, Inc. 5300 Chiron Way Emeryville, CA 94608-2916, USA eric.martin(a)novartis.com<mailto:eric.martin@novartis.com> (510)879-9657

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[Compbio-allhands] 12/3/15 Seminar with Jay Shendure
by Flowers, Nicole 01 Dec '15

01 Dec '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Jay Shendure University of Washington New methods in human genetics December 3, 2015 N. Emami, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Michael Chimenti Referral
by Jacobson, Matt 25 Nov '15

25 Nov '15

- Matt Begin forwarded message: From: Kate Nelson <knelson(a)payettegroup.com<mailto:knelson@payettegroup.com>> Subject: Michael Chimenti Referral Date: November 25, 2015 at 2:26:22 PM PST To: "matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>" <matt.jacobson(a)ucsf.edu<mailto:matt.jacobson@ucsf.edu>> Hi Matt, Michael Chimenti passed along your information. I’m hiring a Principal Bioinformatician in the Bay Area and Michael said that you often circulate job postings via a listserv. It’s a long shot, but I thought I’d pass along the JD in case you wanted to share with your network. JD --> https://goo.gl/o9g5r7 Job description Principal Bioinformatician It was only a matter of time before the big data explosion impacted the food we eat, buy, and sell. We’re the team that wants to make sure that what we think is in our food products, is actually in it. Our analytics platform transforms quality control, analytics, and safety in the global food industry. Built on the foundation of a robust big data engine, our proprietary platform translates quantifiable molecular tests into actionable food data insights. We’re using the same tools and technologies used by clinical genomicists to perform fast and accurate affordable genomic analysis at scale. As our Principal Bioinformatician, you will work directly with the VP of Engineering and be responsible for the development statistical algorithms, methods, and programs for analysis of genomics data. You'll have unparalleled food quality data and domain experts within the company to grow and develop both personally and professionally. With our recent funding, it’s a great time to join us! Food fraud is bigger than ever and this is your chance to solve a real world problem – there is nothing else like this in the world and you could have the opportunity to work on it. Responsibilities • Develop and maintain robust software tools to improve the speed, accuracy, and automation of our analysis pipeline in the cloud • Evaluate third-party tools and libraries we may wish to leverage in our pipeline • Develop novel data analysis and data-mining methods to optimize the performance and accuracy of our platform • Work closely with our science and product team to help define product requirements, spec technical requirements, develop project plans and generate test cases Key responsibilities Requirements • B.S. in Math, Computer Science, Physics, Engineering or equivalent • Minimum 2 years of experience in bioinformatics in industry setting, with strong experience in developing algorithms processing next-generation sequencing data • Familiar with cloud computing and working in cloud environment • Proficiency with SQL and UNIX shells • Proven development experience with an object-oriented language • Strong communication skills both written and verbal with engineers and product marketers • Ability to work independently in a fast paced and high performing environment Preferred Skills • Proven ability to develop algorithms dealing with large-scale data • Extensive experience in biostatistics, advanced mathematics and system modeling • Expertise in Python Thanks in advance and if you have any questions, feel free to reach out! Cheers- Kate Nelson Sr. Technical Recruiter Payette Group 650-326-0760 ext. 104 LinkedIn<https://goo.gl/avPNOa> Twitter<https://goo.gl/GO1Uuw>

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[Compbio-allhands] faculty positions at Shanghaitech, Shanghai
by Andrej Sali 23 Nov '15

23 Nov '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] SAVE THE DATE- PETER KOLLMAN LECTURESHIP- JANUARY 21, 2016
by Flowers, Nicole 19 Nov '15

19 Nov '15

SAVE THE DATE- THURSDAY, January 21, 2016 AT 12:00 PM Michael Gilson UC San Diego PETER A. KOLLMAN LECTURESHIP GENENTECH HALL BYERS AUDITORIUM - UCSF MISSION BAY CAMPUS SIMULCAST TO PARNASSUS CAMPUS S-161 Reception in Byers Hall 3rd Floor Lounge at 3:30 pm. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: Reminder: Janet Iwasa Seminar TODAY 2-3 PM
by Jacobson, Matt 16 Nov '15

16 Nov '15

Not sure if this got sent out to this list - Matt Begin forwarded message: From: "Brewer, Melanie" <Melanie.Brewer(a)ucsf.edu<mailto:Melanie.Brewer@ucsf.edu>> Subject: Reminder: Janet Iwasa Seminar TODAY 2-3 PM Date: November 16, 2015 at 9:15:28 AM PST To: Melanie Bennett Brewer <melaniebbrewer(a)gmail.com<mailto:melaniebbrewer@gmail.com>> Janet Iwasa of the University of Utah will give a HARC-sponsored seminar “Animating Molecules” TODAY Nov. 16, 2-3 PM in Genentech Hall Room N114. Janet is an award-winning animator and TED speaker who uses 3D animation to provide new insights into macromolecular and cellular systems. Come hear about Janet’s work and learn how we might collaborate with her to animate some of the pathways studied in HARC. ------------------------------------------------------- Melanie Bennett Brewer, Ph.D. Program Manager, The HARC Center University of California, San Francisco Genentech Hall S572, MC 2280 600 16th Street San Francisco, CA 94158-2517 HARC Website: harc.ucsf.edu<http://harc.ucsf.edu/> View my publications at Google Scholar<http://scholar.google.com/citations?hl=en&user=HhJKtigAAAAJ&view_op=list_wo…> Connect on: Linked In<https://www.linkedin.com/profile/view?id=35890499&trk=nav_responsive_tab_pr…>

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[Compbio-allhands] faculty jobs at iHuman, ShaghaiTech
by Andrej Sali 11 Nov '15

11 Nov '15

Computational Biology Faculty Positions at the iHuman Institute, ShanghaiTech University The iHuman Institute at ShanghaiTech University was established to understand human cell signaling at a level beyond what is achievable today. The institute encourages interdisciplinary research combining chemistry, biology, imaging, and structural biology of the cellular components involved in signal transduction. Academic basic science and applied industry research is integrated, providing researchers with unique opportunities. The Institute is recruiting 2 regular tenured and/or tenure-track faculty in 2015 in the areas of computer-aided drug design (CADD) and whole cell modeling. Junior level position applicants should have a Ph.D. degree in computational biology/chemistry, as well as 3+ years postdoctoral or industrial experience. Senior position applicants are expected be leading scientists in their research area. The successful applicant will be expected to establish an independent, internationally recognized research program and to hire and supervise postgraduate, graduate and undergraduate students. Each group is encouraged to recruit up to 10 members and be highly collaborative with other laboratories in different disciplines. A strong core infrastructure has been established within the institute to serve the faculty needs. All financial support is provided by the institute. Importantly, grant writing is not required, particularly for junior faculty members so they can focus on creative research and mentoring of their first students. Initial Research Support Package: The Institute will provide internationally competitive start-up funds plus support of Research Associates and Post-Doctoral Fellows up to 10 full time lab members. Research laboratory and office space will be provided to match the research needs. Faculty have access to some of the world’s best research facilities and resources of the Chinese Academy of Science including the National Protein Center, Shanghai Synchrotron, and Chinese National Compound Library. Compensation and Benefits: Starting salary will be competitive at the international level and commensurate with qualifications and experience. We offer a comprehensive benefits package including health benefits as well as subsidized campus housing. The iHuman Institute will also sponsor applications of national and local Talent Programs based on individuals’ qualification and experience. The iHuman Institute is located in Shanghai, China, which is an exciting and rapidly growing global center of excellence for scientific research. Application Procedure: Submit a cover letter, a 2-3 page statement of research interests, a CV and the names and addresses of three individuals who can serve as references to the mail addresses given below: The iHuman Institute ShanghaiTech University, Building 8, 319 Yueyang Road, Shanghai 200031, China Email: iHuman(a)shanghaitech.edu.cn <mailto:iHuman@shanghaitech.edu.cn> Review of applications will start immediately and will continue until positions are filled. For more information, please visit our website: ihuman.shanghaitech.edu.cn -- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org

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[Compbio-allhands] Job openings at Veracyte, South San Francisco
by Seung Joong Kim 10 Nov '15

10 Nov '15

Hi all, Veracyte (South San Francisco) has two job openings in a senior level. 1. DAT: Senior Scientist/Associate Director, Machine Learning 2. R&D Lab: Principal Scientist/Associate Director, Discovery R&D Please see the attached word files for job description. Thanks a lot! About Veracyte Veracyte is pioneering molecular cytology; we are dedicated to helping people avoid unnecessary invasive procedures just to get a diagnosis and to reducing healthcare costs at the same time. We use rigorous science to unlock genomic answers from tiny numbers of cells obtained through minimally invasive methods before surgery is needed. We launched our first product the Afirma® Thyroid FNA Analysis, with a genomic test at its core in record time and have already helped save thousands of patients from unnecessary surgery due to ambiguous thyroid nodule biopsy results. Our genomic test is offered by hundreds of physicians around the country, is covered by Medicare and private payers, and is clinically validated, including in a multicenter study published in the New England Journal of Medicine. Earlier this year, we entered the pulmonology space with the launch of Percepta. The Percepta test uses advanced genomic technology to help patients avoid unnecessary invasive, risky procedures on suspicious lung nodules or lesions that were initially found on computed tomography (CT) scans. Percepta is clinically validated, with its key studies recently published in the New England Journal of Medicine. Looking to our pulmonology pipeline, we are also developing a product to target idiopathic pulmonary fibrosis. The Wall Street Journal named us to its list of top-50 venture capital-funded companies in 2011, BayBio honored us with its Fast Start award in 2012, and In Vivo: The Business and Medicine Report featured us recently as a model for how to build a molecular cytology company. In 2014 and 2015 our employees voted us a Bay Area News Group Top Workplace. Veracyte affords equal employment opportunities to all qualified persons, regardless of race, color, religion, national origin, age, sex, disability, sexual orientation, gender expression, veteran or marital status. Veracyte participates in E-Verify in the United States. - Seung Joong Kim -- Seung Joong Kim, Ph.D. Postdoctoral Scholar, Andrej Sali group Department of Bioengineering and Therapeutic Sciences University of California at San Francisco (UCSF) 1-217-649-2147 http://salilab.org/~sjkim

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[Compbio-allhands] Fwd: DBDS Faculty Search
by Patricia C. Babbitt 09 Nov '15

09 Nov '15

-------- Forwarded Message -------- Subject: DBDS Faculty Search Date: Mon, 9 Nov 2015 17:39:40 +0000 From: Laura Dunkin-Hubby <lhubby(a)stanford.edu> To: babbitt(a)cgl.ucsf.edu <babbitt(a)cgl.ucsf.edu> Dear Dr. Babbitt, I am writing on behalf of Dr. Carlos Bustamante to ask your help in identifying candidates for an Assistant, Associate or Full Professor position in the new Department of Biomedical Data Science (DBDS) at the Stanford University School of Medicine. This appointment will be in the University Tenure Line (UTL). The predominant criterion for appointment in the University Tenure Line is a major commitment to research and teaching. We define biomedical data science as the study of biomedical data and information, of how such data and information may be structured, and of how analysis and processing of biomedical data and information will lead to new discoveries and to advances in health and healthcare. We are particularly interested in candidates dedicated to the development of novel computational and statistical methods for acquiring, representing, storing, analyzing, and applying biological and clinical data at all scales, who can apply their expertise in biomedical informatics and/or biostatistics to meet departmental goals. Further information on the Department of Biomedical Data Science can be found at[dbds.stanford.edu]dbds.stanford.edu. Applicants should have demonstrated strong ability and interest in conducting both methodological and collaborative research, and in teaching. We expect the successful candidate to conduct a vigorous, independent research program, to advise students, and to assist in program administration. Formal teaching in the classroom will be encouraged. An MD, MD/PhD, or PhD in biostatistics, statistics, biomedical informatics, computer science, biomedical engineering or a related area is required. Faculty rank will be determined by the qualifications and experiences of the successful candidate. Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty. It welcomes nominations of and applications from women, members of minority groups, protected veterans and individuals with disabilities, as well as from others who would bring additional dimensions to the university's research, teaching and clinical missions. I would appreciate your forwarding this announcement to individuals whom you feel would be particularly suited for this position. Interested candidates should send a copy of their curriculum vitae, a brief letter outlining their research and teaching interests, and arrange for three letters of reference to be submitted to: Euan Ashley, MD, PhD and Daniel Rubin, MD, MS Search Committee Co-Chairs Department of Biomedical Data Science Stanford University School of Medicine DBDSjobs_SOM(a)stanford.edu<mailto:DBDSjobs_SOM@stanford.edu> Applications will continue to be accepted and considered until the opening is filled. Sincerely yours, Carlos D. Bustamante, PhD Chair, Department of Biomedical Data Science Stanford University School of Medicine - Laura Dunkin-Hubby Administrative Assistant to Dr. Carlos Bustamante Stanford Center for Computational, Evolutionary and Human Genomics T 650.725.5067<file://localhost/tel/+1-650-723-2643> * cehg.stanford.edu -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

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[Compbio-allhands] 11/12/15 Seminar with Xuewu Zhang
by Flowers, Nicole 06 Nov '15

06 Nov '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Xuewu Zhang UT Southwestern Regulation mechanisms of the neuronal axon guidance receptor plexin November 12, 2015 N. Jura, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] Fwd: potential comp chem position at Merck
by Jacobson, Matt 30 Oct '15

30 Oct '15

- Matt Begin forwarded message: From: "McMasters, Daniel R" <daniel_mcmasters(a)merck.com<mailto:daniel_mcmasters@merck.com>> Subject: RE: potential comp chem position at Merck Date: October 30, 2015 at 5:59:45 AM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Thanks! Any help getting the word out to potential candidates is appreciated. We actually have two openings for computational chemists, one each in Boston and West Point, PA (Philadelphia area). There is also an opening for a cheminformatician/comp tox as well as one for a crystallographer. Here are the links for applicants to apply, and of course anyone can feel free to email me at any time. -Daniel Computational chemistry: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… Cheminformatics & computational toxicology: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft… Crystallography: https://merck.taleo.net/careersection/ext_merckunitedstates_en/jobdetail.ft…

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[Compbio-allhands] Fwd: Still open places for our course on modeling 3D genomes and genomic domains
by Andrej Sali 30 Oct '15

30 Oct '15

-- Andrej Sali, Ph.D. Professor, Department of Bioengineering and Therapeutic Sciences Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences University of California, San Francisco UCSF MC 2552 Byers Hall Room 503B 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Administrative Assistant: Steve Ha, assistant(a)salilab.org, Tel +1 (415) 514-4228, 502-8084 Email sali(a)salilab.org; Web http://salilab.org > Begin forwarded message: > > From: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Date: October 30, 2015 at 11:27:49 AM PDT > To: "Marc A. Marti-Renom" <martirenom(a)cnag.crg.eu> > Subject: Still open places for our course on modeling 3D genomes and genomic domains > > Dear Friends and Colleagues, > > Apologies for the mass posting. > > We still have open positions for people who may be interested in our TADbit Course at the Gulbenkian Institute in Oeiras (near Lisbon) in Portugal. > > See the details here http://gtpb.igc.gulbenkian.pt/bicourses/CSDM15/ <http://gtpb.igc.gulbenkian.pt/bicourses/CSDM15/> or in the attached poster. > > Pass it along to whom you may think could be interested. > > Thanks in advance! > Marc A. Marti-Renom > > > > > ... > Marc A. Marti-Renom, ICREA Research Professor > Structural Genomics Group Leader > Centre Nacional d’Anàlisi Genòmica - Centre de Regulació Genòmica (CNAG-CRG) > Parc Científic de Barcelona – Torre I (10th floor) > Baldiri Reixac, 4, 08028 Barcelona > Tel +34 9340 33743 > Email: martirenom(a)cnag.crg.eu <mailto:martirenom@cnag.crg.eu> > Web: http://marciuslab.org <http://marciuslab.org/> · http://cnag.crg.eu <http://cnag.crg.eu/> · http://crg.cat <http://crg.cat/> > > *** Consider the environment. Print responsibly. *** > > CRG/”la Caixa” – Severo Ochoa FELLOWSHIPS AVAILABLE TO CARRY OUT PhD > STUDIES AT THE CENTER FOR GENOMIC REGULATION (CRG), BARCELONA > MORE INFORMATION AND ONLINE APPLICATION AT: http:// <http://www.crg.eu/lacaixa_fellowships>www.crg.eu/lacaixa_fellowships <http://www.crg.eu/lacaixa_fellowships> > > > > > > > > > > > > > >

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[Compbio-allhands] Fwd: The Rockefeller University - Fellow Position
by Jacobson, Matt 30 Oct '15

30 Oct '15

- Matt Begin forwarded message: From: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Subject: The Rockefeller University - Fellow Position Date: October 30, 2015 at 9:44:01 AM PDT To: "Melanie J. Lee" <leem(a)mail.rockefeller.edu<mailto:leem@mail.rockefeller.edu>> Dear Colleague: The Center for Studies in Physics and Biology, at The Rockefeller University, expects to have a small number of postdoctoral fellowships available for appointments in September 2016. We are seeking theoretical physicists, mathematicians and computer scientists with a demonstrable interest in the interface between their discipline and biology. The Fellows are to be at that stage of career as to function as independent members of the Center, free to work alone or in collaboration with any members of The Rockefeller University faculty. Would you be so kind as to post the attached notice, and share this within your department and with your peers and colleagues. Many thanks! Melanie J. Lee Administrative Assistant Center for Studies in Physics and Biology Rockefeller University 1230 York Avenue New York, NY 10065-6399 Tel: 212-327-8636 Fax: 212-327-8544

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[Compbio-allhands] Fwd: open CC position
by Jacobson, Matt 29 Oct '15

29 Oct '15

- Matt Begin forwarded message: From: "Lexa, Katrina W" <katrina.lexa(a)merck.com<mailto:katrina.lexa@merck.com>> Subject: open CC position Date: October 29, 2015 at 1:45:42 PM PDT To: "Jacobson, Matt" <Matt.Jacobson(a)ucsf.edu<mailto:Matt.Jacobson@ucsf.edu>> Hi Matt, Another comp chemist job ad went up for the Structural Chemistry dept – they are looking primarily for people coming out of a postdoc. https://taleo.msd.com/careersection/merck_external_career_section/jobdetail… They are hoping to fill several slots, so please pass along. Thanks! ------------------------------- Katrina Lexa Merck & Co., Inc. 126 East Lincoln Ave RY800-C364 Rahway, NJ 07065 phone: (732) 594-7058 office: RY800-D365 Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (2000 Galloping Hill Road, Kenilworth, New Jersey, USA 07033), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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[Compbio-allhands] Volunteers needed to help with upcoming Software Carpentry workshops at UCSF on R and Python
by Patricia C. Babbitt 28 Oct '15

28 Oct '15

Hi all, The UCSF Institute for Computational Health Sciences and the UCSF Library have set up a collaboration to bring in Software Carpentry to teach two bootcamp workshops, one an R and the other on Python on Nov. 20 and 21. The content is geared to grad students and postdocs who want to develop basic skills with these tools. Both will run for two days, 9 am to 5 pm. Volunteers are needed to help the Software Carpentry Instructors in providing assistance to workshop learners during practical sessions. While not a paid gig, breakfast and coffee/snacks will be offered in the afternoon of each day. You will be listed on the workshop materials and website as helpers and you can put this effort on your CV as service to the UCSF community and to show you have teaching experience in these areas. You can check out a similar recent boot camp to get a feel for the content and whether your expertise is a good fit: https://richford.github.io/2015-10-22-uw/ The roles for the helpers are described at https://software-carpentry.org/workshops/checklists/helpers.html If you're interested in doing this, please send an email to babbitt(a)cgl.ucsf.edu. I'm happy to answer questions you may have before deciding if you want to sign up for this. We'll take folks who are a fit on a first come, first served basis. If you decide to participate, we will also ask for your feedback on the experience, as having some expert eyes on the content and format of the boot camps and syllabi will be helpful for future workshops we want to mount on biostats and bioinformatics for the broad UCSF community. Getting your opinions about how best to do that would be helpful to us. If you're interested in participating as instructors in some of these later workshops, please let me know that as well. Thanks. Patsy Babbitt -- Patricia Babbitt Professor, Department of Bioengineering & Therapeutic Sciences and Department of Pharmaceutical Chemistry California Institute for Quantitative Biosciences Director, Graduate Program in Biological & Medical Informatics University of California, San Francisco UCSF MC 2550 Byers Hall Room508E 1700 4th Street San Francisco, CA 94143, USA Tel +1 (415) 476-3784 Fax +1 415-502-8193 Email: babbitt(a)cgl.ucsf.edu; Web http://babbittlab.ucsf.edu/ Assistant: Ms. Josel Tongson, +1 415-514-1214, 415-514-4861 GraciaJoselina.Tongson(a)ucsf.edu

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[Compbio-allhands] Fwd: Tenure-Track Openings in Computational Biology at Carnegie Mellon University
by Jacobson, Matt 25 Oct '15

25 Oct '15

-- Matt Sent from my iPhone Begin forwarded message: From: "Robert F. Murphy" <murphy(a)cmu.edu<mailto:murphy@cmu.edu>> Date: October 25, 2015 at 5:15:54 PM PDT Subject: Re: Tenure-Track Openings in Computational Biology at Carnegie Mellon University ======================================== Tenure-track Faculty Positions Available We seek outstanding researchers who are developing and applying rigorous computational methods in all areas of biology for tenure-track positions in the Computational Biology Department within the School of Computer Science. We especially seek candidates working on automated analysis and modeling of biological and medical images, and those addressing problems in neurobiology using computational methods, although outstanding candidates from all areas will be enthusiastically considered. The department has extensive strengths in methods underlying genome-based personalized medicine (genome association for complex phenotypes, dynamic network models, efficient sequence analysis), bioimage informatics (analysis and modeling of cell and tissue organization, perturbation and differentiation), modeling and simulation of biological systems at various levels, and application of active machine learning to biological problems. A critical focus is that we do not simply build systems to reproduce or automate tasks that humans can do, but build machine learning and vision systems that answer questions and build models in ways well beyond human capabilities and that can be the driver behind choice of further experiments. Additional information on the department may be found at http://www.cbd.cmu.edu. We particularly encourage applications from candidates who have a demonstrated track record in mentoring and nurturing female and under-represented minority students. Appointments will be made either entirely in the Computational Biology Department or jointly with other departments in the University (as appropriate to the background and interests of the candidate and at a level commensurate with experience). New faculty members will be expected to both contribute to and benefit from the collaborative spirit that is a hallmark of Carnegie Mellon University and from opportunities to collaborate with other institutions in the Pittsburgh region. Applications should be submitted through the faculty application system at https://webapps.cs.cmu.edu/FacultyApplication/SCS/Welcome. Completed applications must be received by January 4, 2016. Carnegie Mellon is an EEO/Affirmative Action Employer - M/F/Disability/Veteran ======================= Robert F. Murphy, Ph.D. Ray and Stephanie Lane Professor of Computational Biology and Professor of Biological Sciences, Biomedical Engineering, and Machine Learning Head, Computational Biology Department, School of Computer Science, Carnegie Mellon University 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 Phone: 412-268-3480, FAX: 412-268-2977, email: murphy(a)cmu.edu<mailto:murphy@cmu.edu>, Skype: rfmurphy1953 Personal Home Page: http://www.andrew.cmu.edu/user/murphy Honorary Professor, University of Freiburg and External Senior Fellow, Freiburg Institute for Advanced Studies

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[Compbio-allhands] 10/29/15 Seminar with Chris Garcia
by Flowers, Nicole 23 Oct '15

23 Oct '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Chris Garcia Stanford Turning cell surface receptor signaling through ligand engineering: Type I receptors versus GPCR October 29, 2015 J. Kung, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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[Compbio-allhands] 10/22/15 Seminar with Andrew Ward
by Flowers, Nicole 16 Oct '15

16 Oct '15

BBC Graduate Programs Seminar Series Bioinformatics Biophysics Chemistry & Chemical Biology Complex Biological Systems Thursdays, 12 Noon Genentech Hall Auditorium Simulcast to Parnassus Campus S-161 (Please note: A lack of attendance in S-161 within the first 10 minutes of the start time will result in a cancellation of the simulcast.) Andrew Ward Scripps High-resolution cryoEM structures of viral glycoproteins and neutralizing antibodies October 22, 2015 W. DeGrado, Host BBC Seminars are supported by the Biophysics, Bioinformatics, and Chemistry & Chemical Biology IFM, Department of Pharmaceutical Chemistry, QBC, HARC Center, the Center for Systems and Synthetic Biology, and the Quantitative Student Group Series. Nicole Takesono Flowers BMI, BP, CCB, & PSPG Graduate Program Assistant UCSF MC 2280 600 16th St. Genentech Hall Room 522 San Francisco, CA 94143 Phone: (415) 502-6518 Fax: (415) 514-1546

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